PMC:6599329 / 8010-14082 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/6599329","sourcedb":"PMC","sourceid":"6599329","source_url":"https://www.ncbi.nlm.nih.gov/pmc/6599329","text":"Biological processes\nThe proteins were clustered based on gene ontology (GO) analysis and its relative expression at planktonic and biofilm stages were analyzed. Comparative proteome analysis revealed that several ribosomal proteins and proteins involved in DNA replication and transcription were found to be normally expressed or slightly upregulated. The relative abundance of some proteins involved in nucleotide metabolism and protein biosynthesis was affected to differing degrees under biofilm conditions. Major functional categories of proteins upregulated in biofilm stages are listed in Table 1.\nTable 1 List of proteins enhanced in biofilm stages of E. faecalis SK460\nNCBI-ID Pathways/cellular processes\nAmino acid metabolism\n NP_816782.1 Succinyl-diaminopimelate desuccinylase (EF_3178)\n NP_816328.1 MTA/SAH nucleosidase (pfs)\n NP_815300.1 Cysteine synthase A (cysK)\n NP_815281.1 Chorismate synthase (aroC)\n NP_815821.1 Glutamine synthetase, type I (glnA)\n NP_814529.1 S-adenosylmethionine synthetase (metK)\n NP_815283.1 3-phosphoshikimate 1-carboxyvinyltransferase (aroA)\n NP_816193.1 Serine hydroxymethyltransferase (glyA)\n NP_816069.1 Threonine synthase (thrC)\n NP_815279.1 3-deoxy-7-phosphoheptulonate synthase (EF_1562)\n NP_816700.1 Bifunctional glutamate--cysteine ligase/glutathione synthetase (gshF)\n NP_816650.1 Glutamyl-aminopeptidase (pepA)\n NP_814940.1 Acetolactate synthase (EF_1213)\n NP_815294.1 Dihydrofolate reductase (folA)\nGlycolysis, citric acid cycle, pentose phosphate pathway\n NP_815638.1 Triosephosphate isomerase (tpiA)\n NP_815639.1 Phosphoglycerate kinase (pgk)\n NP_814897.1 Fructose-bisphosphate aldolase (fba)\n NP_813994.1 Phosphoglycerate mutase (gpmA)\n NP_815245.1 Glyceraldehyde 3-phosphate dehydrogenase (gap-1)\n NP_815637.1 Enolase (eno)\n NP_815137.1 Glucose-6-phosphate isomerase (pgi)\n NP_815075.1 Pyruvate dehydrogenase complex, E1 component subunit beta (pdhB)\n NP_815076.1 Dihydrolipoamide acetyltransferase (aceF)\n NP_816104.1 Pyruvate carboxylase (pycA)\n NP_813976.1 Deoxyribose-phosphate aldolase (deoC)\n NP_813986.1 Phosphopentomutase (deoB)\n NP_814782.1 6-phosphogluconate dehydrogenase (gnd)\nStress response, chaperones and DNA repair\n NP_814237.1 OsmC/Ohr family protein (EF_0453)\n NP_816831.1 Dps family protein (EF_3233)\n NP_816649.1 Thioredoxin family protein (EF_3036)\n NP_814938.1 NADH peroxidase (npr)\n NP_815447.1 General stress protein (EF_1744)\n NP_816369.1 Alkyl hydroperoxide reductase subunit C (ahpC)\n NP_813885.1 gls24 protein\n NP_816648.1 Universal stress protein (EF_3035)\n NP_816867.1 Glutathione reductase (gor)\n NP_816700.1 Bifunctional glutamate--cysteine ligase/glutathione synthetase (gshF)\n NP_816368.1 Thioredoxin reductase/glutathione-like protein (EF_2738)\n NP_814049.1 L-lactate dehydrogenase (ldh1)\n NP_816550.1 AhpC/TSA family protein (EF_2932)\n NP_815246.2 GTPase ObgE\n NP_815059.1 Thioredoxin reductase (trxB)\n NP_815353.1 Transcriptional repressor CodY (codY)\n NP_816010.1 ATP-dependent Clp protease, ATP-binding protein ClpB (clpB)\n NP_814518.1 ATP-dependent Clp protease proteolytic subunit (clpP)\n NP_816516.1 Cyclophilin type peptidyl-prolyl cis-trans isomerase (EF_2898)\n NP_814457.1 ATP-dependent Clp protease, ATP-binding protein ClpE (clpE)\n NP_816532.1 Transcription elongation factor GreA\n NP_815030.1 dnak protein\n NP_815032.1 dnaJ protein\n NP_815029.1 Heat shock protein GrpE (grpE)\n NP_814465.1 Trigger factor (TIG)\n NP_816273.1 GroS (10 kDa chaperonin)\n NP_816272.1 GroL(60 kDa chaperonin)\n NP_814060.1 Fn1610 (33 kDa chaperonin) (hslO)\n NP_814686.1 Uracil-DNA glycosylase (ung)\n NP_814720.1 DNA repair protein RecN (recN)\nRhamnose biosynthesis\n NP_815854.1 dTDP-glucose 4,6-dehydratase (rfbB)\n NP_815853.1 dTDP-4-dehydrorhamnose reductase (EF_2191)\n NP_815856.1 Glucose-1-phosphate thymidylyltransferase (rfbA)\nArginine metabolism\n NP_813908.1 Ornithine carbamoyltransferase (arcB)\n NP_815423.1 Carbamoyl phosphate synthase small subunit (carA)\n NP_814373.1 Ornithine cyclodeaminase (EF_0616)\n NP_813909.1 Carbamate kinase (arcC1)\n NP_813907.1 Arginine deiminase (arcA)\n NP_814719.1 ArgR family transcriptional regulator (EF_0983)\nQuorum sensing and pheromone associated lipoprotein\n NP_814911.1 S-ribosylhomocysteinase (luxS)\n NP_816853.1 Pheromone cAD1 lipoprotein (EF_3256)\n NP_814793.1 Pheromone binding protein (EF_1060)\n NP_815061.1 Pheromone cAM373 lipoprotein (EF_1340)\nAdhesion associated proteins\n NP_814266.1 Aggregation substance (EF_0485)\n NP_814342.1 Adhesion lipoprotein (EF_0577)\n NP_814975.1 Fibronectin/fibrinogen binding protein (EF_1249)\nAutolysin and D-Alanylation of teichoic acid\n NP_814543.1 Autolysin (EF_0799)\n NP_816376.1 D-alanine--poly(phosphoribitol) ligase subunit 2 (dltC)\n NP_816375.1 dltD protein (dltD)\nIn general, major glycolytic enzymes and several enzymes in the citric acid cycle and pentose phosphate pathway were found to be in higher abundance in biofilm stages of SK460. Enzymes involved in rhamnose biosynthesis which forms the part of enterococcal polysaccharide antigen gene cluster was also found to be upregulated in biofilm stages. Compared to planktonic forms, Enterococcal biofilms showed a hike in stress response factors, DNA repair system, molecular chaperones, pheromone associated lipoproteins and other adhesion associated proteins. Besides, the present proteome analysis established the role of luxS mediated quorum sensing in enterococcal biofilm development.\nSTRING analysis predicted the molecular interactions among the highly expressed proteins in biofilm stages with enrichment p-value \u003c 1.0e-16 and is shown in Fig. 3. The functional interactome of the whole upregulated protein sets is depicted in Additional file 2: Figure S2.\nFig. 3 STRING analysis (Version 10.5) showing the predicted molecular action among the upregulated proteins in biofilm stages. The gene nomenclatures are depicted in Table 1. Colored nodes: query proteins and first shell of interactors. Empty nodes: proteins of unknown 3D structure. Filled nodes: 3D structure is known/predicted. 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